Data from: Powerful methods for detecting introgressed regions from population genomic data

Understanding the types and functions of genes that are able to cross species boundaries—and those that are not—is an important step in understanding the forces maintaining species as largely independent lineages across the remainder of the genome. With large next-generation sequencing data sets we are now able to ask whether introgression has occurred across the genome, and multiple methods have been proposed to detect the signature of such events. Here, we introduce a new summary statistic that can be used to test for introgression, RNDmin, that makes use of the minimum pairwise sequence distance between two population samples relative to divergence to an outgroup. We find that our method offers a modest increase in power over other, related tests, but that all such tests have high power to detect introgressed loci when migration is recent and strong. RNDmin is robust to variation in the mutation rate, and remains reliable even when estimates of the divergence time between sister species are inaccurate. We apply RNDmin to population genomic data from the African mosquitoes Anopheles quadriannulatus and A. arabiensis, identifying three novel candidate regions for introgression. Interestingly, one of the introgressed loci is on the X chromosome, but outside of an inversion separating these two species. Our results suggest that significant, but rare, sharing of alleles is occurring between species that diverged more than 1 million years ago, and that application of these methods to additional systems are likely to reveal similar results.

探明可跨物种边界的基因与不可跨物种边界的基因的类型与功能，是解析基因组其余区域中维持物种作为相对独立演化支系的演化动力的关键一环。依托大规模下一代测序（next-generation sequencing）数据集，我们如今得以探究全基因组范围内是否发生了基因渐渗（introgression），目前已有多种方法被提出以检测这类事件的分子信号。在此，我们提出一种可用于检测基因渐渗的新型汇总统计量RNDmin，该统计量基于两个种群样本间的最小成对序列距离，并结合其与外类群的分化水平进行计算。研究发现，相较于其他同类检验方法，本方法的检验效力仅略有提升；但当基因流近期且强烈时，所有这类检验方法均能高效检测到渐渗位点（introgressed loci）。RNDmin对突变率的波动具有鲁棒性，即便姊妹物种间分化时间的估算存在偏差，该方法仍能保持可靠的检验性能。我们将RNDmin应用于非洲按蚊（Anopheles quadriannulatus）与阿拉伯按蚊（A. arabiensis）的种群基因组数据，成功鉴定出三个全新的基因渐渗候选区域。值得注意的是，其中一个渐渗位点位于X染色体上，却处于区分这两个物种的染色体倒位区域之外。本研究结果表明，在分化时长超过100万年的物种之间，正发生着程度显著但频率较低的等位基因共享现象；且将这类检验方法应用于其他研究系统时，大概率会得到类似的结论。